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GeneBe API Showcase
This page demonstrates how to use the GeneBe API to query variant information. The API provides programmatic access to genomic annotations and variant data.
API presented here should be used for checking single variants. If you want to check many variants at once, please use other API endpoints that you will find in the documentation.
Documentation & Advanced Usage
• Complete API documentation:docs.genebe.net/docs/api/overview/
• Interactive endpoint tester:api.genebe.net/cloud/gb-api-doc/swagger-ui/
• Python client for pandas:pypi.org/project/genebe/
• Java CLI for VCF files:github.com/pstawinski/genebe-cli
• All tools documented at:docs.genebe.net
API Request Examples for Variant: 10-122986950-A-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=10&pos=122986950&ref=A&alt=C&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 4,
"criteria": [
"BP4_Strong"
],
"effects": [
"missense_variant"
],
"gene_symbol": "PSTK",
"hgnc_id": 28578,
"hgvs_c": "c.865A>C",
"hgvs_p": "p.Lys289Gln",
"inheritance_mode": "AR",
"pathogenic_score": 0,
"score": -4,
"transcript": "NM_001363531.2",
"verdict": "Likely_benign"
}
],
"acmg_classification": "Likely_benign",
"acmg_criteria": "BP4_Strong",
"acmg_score": -4,
"allele_count_reference_population": 24,
"alphamissense_prediction": null,
"alphamissense_score": 0.1226,
"alt": "C",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Benign",
"bayesdelnoaf_score": -0.33,
"chr": "10",
"clinvar_classification": "Uncertain significance",
"clinvar_disease": "not specified",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"computational_prediction_selected": "Benign",
"computational_score_selected": 0.05356484651565552,
"computational_source_selected": "MetaRNN",
"consequences": [
{
"aa_alt": "Q",
"aa_end": null,
"aa_length": 358,
"aa_ref": "K",
"aa_start": 289,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1173,
"cdna_start": 944,
"cds_end": null,
"cds_length": 1077,
"cds_start": 865,
"consequences": [
"missense_variant"
],
"exon_count": 6,
"exon_rank": 5,
"exon_rank_end": null,
"feature": "NM_001363531.2",
"gene_hgnc_id": 28578,
"gene_symbol": "PSTK",
"hgvs_c": "c.865A>C",
"hgvs_p": "p.Lys289Gln",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000406217.8",
"protein_coding": true,
"protein_id": "NP_001350460.1",
"strand": true,
"transcript": "NM_001363531.2",
"transcript_support_level": null
},
{
"aa_alt": "Q",
"aa_end": null,
"aa_length": 358,
"aa_ref": "K",
"aa_start": 289,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 1173,
"cdna_start": 944,
"cds_end": null,
"cds_length": 1077,
"cds_start": 865,
"consequences": [
"missense_variant"
],
"exon_count": 6,
"exon_rank": 5,
"exon_rank_end": null,
"feature": "ENST00000406217.8",
"gene_hgnc_id": 28578,
"gene_symbol": "PSTK",
"hgvs_c": "c.865A>C",
"hgvs_p": "p.Lys289Gln",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_001363531.2",
"protein_coding": true,
"protein_id": "ENSP00000384653.3",
"strand": true,
"transcript": "ENST00000406217.8",
"transcript_support_level": 5
},
{
"aa_alt": "Q",
"aa_end": null,
"aa_length": 348,
"aa_ref": "K",
"aa_start": 289,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1705,
"cdna_start": 1305,
"cds_end": null,
"cds_length": 1047,
"cds_start": 865,
"consequences": [
"missense_variant"
],
"exon_count": 7,
"exon_rank": 5,
"exon_rank_end": null,
"feature": "ENST00000368887.7",
"gene_hgnc_id": 28578,
"gene_symbol": "PSTK",
"hgvs_c": "c.865A>C",
"hgvs_p": "p.Lys289Gln",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000357882.3",
"strand": true,
"transcript": "ENST00000368887.7",
"transcript_support_level": 1
},
{
"aa_alt": "Q",
"aa_end": null,
"aa_length": 348,
"aa_ref": "K",
"aa_start": 289,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1344,
"cdna_start": 944,
"cds_end": null,
"cds_length": 1047,
"cds_start": 865,
"consequences": [
"missense_variant"
],
"exon_count": 7,
"exon_rank": 5,
"exon_rank_end": null,
"feature": "NM_153336.3",
"gene_hgnc_id": 28578,
"gene_symbol": "PSTK",
"hgvs_c": "c.865A>C",
"hgvs_p": "p.Lys289Gln",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_699167.2",
"strand": true,
"transcript": "NM_153336.3",
"transcript_support_level": null
},
{
"aa_alt": "Q",
"aa_end": null,
"aa_length": 348,
"aa_ref": "K",
"aa_start": 289,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1047,
"cdna_start": 865,
"cds_end": null,
"cds_length": 1047,
"cds_start": 865,
"consequences": [
"missense_variant"
],
"exon_count": 6,
"exon_rank": 5,
"exon_rank_end": null,
"feature": "ENST00000405485.2",
"gene_hgnc_id": 28578,
"gene_symbol": "PSTK",
"hgvs_c": "c.865A>C",
"hgvs_p": "p.Lys289Gln",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000384764.2",
"strand": true,
"transcript": "ENST00000405485.2",
"transcript_support_level": 2
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 236,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1003,
"cdna_start": null,
"cds_end": null,
"cds_length": 711,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 4,
"exon_rank": null,
"exon_rank_end": null,
"feature": "XM_017015641.3",
"gene_hgnc_id": 28578,
"gene_symbol": "PSTK",
"hgvs_c": "c.708-3224A>C",
"hgvs_p": null,
"intron_rank": 3,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_016871130.1",
"strand": true,
"transcript": "XM_017015641.3",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 818,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 5,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "ENST00000465232.5",
"gene_hgnc_id": 28578,
"gene_symbol": "PSTK",
"hgvs_c": "n.589A>C",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": true,
"transcript": "ENST00000465232.5",
"transcript_support_level": 3
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 696,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 5,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "ENST00000483455.5",
"gene_hgnc_id": 28578,
"gene_symbol": "PSTK",
"hgvs_c": "n.522A>C",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": true,
"transcript": "ENST00000483455.5",
"transcript_support_level": 3
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 872,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 5,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "ENST00000496079.1",
"gene_hgnc_id": 28578,
"gene_symbol": "PSTK",
"hgvs_c": "n.339A>C",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": true,
"transcript": "ENST00000496079.1",
"transcript_support_level": 3
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 2210,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 7,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "ENST00000497219.5",
"gene_hgnc_id": 28578,
"gene_symbol": "PSTK",
"hgvs_c": "n.1398A>C",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": true,
"transcript": "ENST00000497219.5",
"transcript_support_level": 2
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 1349,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 7,
"exon_rank": 5,
"exon_rank_end": null,
"feature": "XR_001747018.2",
"gene_hgnc_id": 28578,
"gene_symbol": "PSTK",
"hgvs_c": "n.944A>C",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": true,
"transcript": "XR_001747018.2",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 602,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 4,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000483755.5",
"gene_hgnc_id": 28578,
"gene_symbol": "PSTK",
"hgvs_c": "n.383+575A>C",
"hgvs_p": null,
"intron_rank": 3,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": true,
"transcript": "ENST00000483755.5",
"transcript_support_level": 5
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs569209094",
"effect": "missense_variant",
"frequency_reference_population": 0.000014961661,
"gene_hgnc_id": 28578,
"gene_symbol": "PSTK",
"gnomad_exomes_ac": 19,
"gnomad_exomes_af": 0.0000130876,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_ac": 5,
"gnomad_genomes_af": 0.0000328196,
"gnomad_genomes_homalt": 0,
"gnomad_mito_heteroplasmic": null,
"gnomad_mito_homoplasmic": null,
"hom_count_reference_population": 0,
"mitotip_prediction": null,
"mitotip_score": null,
"pathogenicity_classification_combined": "Uncertain significance",
"phenotype_combined": "not specified",
"phylop100way_prediction": "Uncertain_significance",
"phylop100way_score": 5.328,
"pos": 122986950,
"ref": "A",
"revel_prediction": "Benign",
"revel_score": 0.083,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0.019999999552965164,
"splice_source_selected": "max_spliceai",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0.02,
"transcript": "NM_001363531.2"
}
]
}